To my memory the story threads weren't being laid down until the very end of 2.3 - when we got our first whiff of Lady Iceheart (Ysayle) stealing a crystal shipment and (I believe) the stinger showing Lahabrea influencing Archbishop Thordan in some manner. You gotta remember 1.X bombed due for a multitude of reasons and A Realm Reborn was a big risk on SE's part - kind of why 2.1 - 2.3 is pretty much just filler, fighting monsters of the week (Moggle Mog, Leviathan, and Ramuh) with a political intrigue story that is given an unsatisfying conclusion halfway through Heavensward after a series of narrative disruptions. Until Yoshi-P proved XIV could be successful, the suits didn't want to invest too much in it.

I don't feel like arguing over Gaius' philosophy, and given the Twelve have been proven to exist in some capacity and not as primals...